Versions and Availability

Softenv Keys for ImageMagick on tezpur

▶ Softenv FAQ?

Shells

A user may choose between using /bin/bash
and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if
they exist (in order):

~/.bash_profile (anything sent to STDOUT or STDERR
will cause things like rsync to break)

~/.bashrc (interactive login only)

~/.profile

When a user logs out of an interactive session, the
file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is
set automatically using SoftEnv. See below for more
information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's
environment if his login shell is /bin/tcsh.

Softenv

SoftEnv is a utility that is supposed to help users manage complex
user environments with potentially conflicting application versions
and libraries.

System Default Path

When a user logs in, the system /etc/profile
or /etc/csh.cshrc (depending on login shell, and mirrored
from csm:/cfmroot/etc/profile)
calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to
set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the
variables and paths accordingly.

Viewing Available Packages

The command softenv will provide a list of
available packages. The listing will look something like:

Managing SoftEnv

The file ~/.soft in the user's home directory is where
the different packages are managed. Add the +keyword into your .soft
file. For instance, ff one wants to add the Amber Molecular Dynamics
package into their environment, the end of the .soft file should look
like this:

+amber-8

@default

To update the environment after modifying this file, one simply
uses the resoft command:

% resoft

The command soft can be used to manipulate the environment
from the command line. It takes the form:

$ soft add/delete +keyword

Using this method of adding or removing keywords requires the user
to pay attention to possible order dependencies. That is, best results
require the user to remove keywords in the reverse order in which they
were added. It is handy to test out individual keys, but can lead to
trouble if changing multiple keys. Changing the .soft file and
issuing the resoft is the recommended way of dealing with
multiple changes.

Usage

An X-Windows session must be used in order to view any of the
graphical output, but the command line tools can be used to process
files without display.

▶ X11 FAQ?

From *nix

Since ssh and X11 are already on most client machines running some
sort of unix (Linux, FreeBSD, etc), one would simply use the following
command:

% ssh -X -Y username@remote.host.tdl

Once successfully logged in, the following command should open a
new terminal window on the local host:

From Mac OS X

An X11 service is not installed by default, but one is available
for installation on the OS distribution disks as an add-on. An
alternative would be to install the XQuartz version. Make sure the X11
application is running and connect to the cluster using:

% ssh -X -Y username@remote.host.tdl

From Windows

Microsoft Windows does not provide an X11 server, but there are
both open source and commercial versions available. You also need to
install an SSH client. Recommended applications are:

Note About Cygwin

Cygwin is still a useful environment, but is to complicated and
contains too many unnecessary parts when all one wants is to interface
with remote X11 sessions. For these reasons, we recommend Xming and
PuTTY as listed above.

Advanced Usage

The most important connection that is made is from the user's
client machine to the first remote host. One may "nest" X11
forwarding by using the ssh -XY command
to jump to other remote hosts.

For example:

1. on client PC (*nix or Windows), ssh to remotehost1

2. on remotehost1 (presumably a *nix machine), ssh -XY to remotehost2

3. on remotehost2 (presumably a *nix machine), ssh -XY to remotehost3

...

8. on remotehost8 (presumably a *nix machine), ssh -XY to remotehost9

9. on remotehost9, running an X11 application like xtermshould propagate the remote window back to the initial client PC through all of the additional remote connects.

Note that ImageMagick is actually a suite of related programs. One
common operation is to convert an image file from one
format to another, say from JPeg to PNG: